8JCY: PDB entry 8JCY

Cryo-EM structure of mGlu2-mGlu3 heterodimer in presence of LY341495, NAM563, and LY2389575 (dimerization mode I). Determined by electron microscopy at 2.9 Å resolution. Released 21 Jun 2023.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 10,874
Mol. weight: 225.97 kDa
Ligands: CLR, Z99, NAG
Released: 21 Jun 2023

Explore 8JCY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JCY contains 58 α-helices and 46 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 2: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	26-28	3	1
β-strand	32-38	7	1
β-strand	41-43	3	2
β-strand	50-53	4	2
α-helix	54	1
α-helix	55-59	5
α-helix	60-73	14
α-helix	82-83	2
β-strand	84-90	7	1
α-helix	95-102	8
α-helix	105-109	5
β-strand	136-141	6	1
α-helix	145-156	12
β-strand	162-164	3	1
α-helix	170-172	3
β-strand	181-183	3	1
α-helix	188-201	14
β-strand	206-207	2	3
β-strand	208-212	5	4
α-helix	215-229	15
β-strand	234-235	2	3
β-strand	239-241	3	4
α-helix	247-258	12
β-strand	265-268	4	4
α-helix	272-284	13
β-strand	290-293	4	4
β-strand	315-319	5	4
α-helix	325-332	8
α-helix	345-352	8
α-helix	378-399	22
α-helix	408-410	3
α-helix	415-417	3
α-helix	418-423	6
β-strand	428-429	2	5
α-helix	430	1
β-strand	440-441	2	5
β-strand	453-460	8	4
β-strand	466-474	9	4
β-strand	478	1	4
α-helix	486-488	3
β-strand	510-512	3	6
β-strand	521-522	2	6
α-helix	524-526	3
β-strand	530-531	2	7
β-strand	537-538	2	7
α-helix	569-590	22
α-helix	596-600	5
α-helix	603-624	22
α-helix	626-627	2
α-helix	629-658	30
α-helix	676-700	25
α-helix	726-748	23
α-helix	756-783	28
α-helix	787-807	21
α-helix	810-818	9

Chain 3: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	33-35	3	8
β-strand	39-45	7	8
β-strand	48-50	3	9
β-strand	57-60	4	9
α-helix	62-67	6
α-helix	68-81	14
α-helix	90	1
β-strand	91-97	7	8
α-helix	102-114	13
β-strand	142-147	6	8
α-helix	151-161	11
β-strand	168-170	3	8
α-helix	176-179	4
β-strand	187-189	3	8
α-helix	197-207	11
β-strand	212-218	7	10
α-helix	222-236	15
β-strand	240-247	8	10
α-helix	255-264	10
β-strand	271-274	4	10
α-helix	278-290	13
β-strand	296-299	4	10
β-strand	321-325	5	10
α-helix	331-338	8
α-helix	351-359	9
β-strand	361-362	2	11
β-strand	371-372	2	11
α-helix	373-374	2
α-helix	390-411	22
α-helix	427-429	3
α-helix	430-434	5
α-helix	435-437	3
β-strand	440-441	2	12
β-strand	453-454	2	12
β-strand	465-473	9	10
β-strand	478-487	10	10
β-strand	490-492	3	10
β-strand	518-519	2	13
β-strand	532-533	2	13
α-helix	539-540	2
α-helix	564-567	4
α-helix	575-600	26
α-helix	611-632	22
α-helix	641-664	24
α-helix	683-705	23
α-helix	706-708	3
α-helix	734-757	24
α-helix	765-791	27
α-helix	797-825	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A	2	protein	993	Homo sapiens	P62942 (AlphaFold model), Q14416 (AlphaFold model)
Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR	3	protein	993	Homo sapiens	A0A8V8TRG9, Q14832 (AlphaFold model)

Sequence of entity 1 (2), FASTA

>8JCY_1 Metabotropic glutamate receptor 2,Peptidyl-prolyl cis-trans isomerase FKBP1A (chains 2)
DYKDDDDGAPEGPAKKVLTLEGDLVLGGLFPVHQKGGPAEDCGPVNEHRGIQRLEAMLFA
LDRINRDPHLLPGVRLGAHILDSCSKDTHALEQALDFVRASLSRGADGSRHICPDGSYAT
HGDAPTAITGVIGGSYSDVSIQVANLLRLFQIPQISYASTSAKLSDKSRYDYFARTVPPD
FFQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFELEARARNICVATSEKVGRAMSRA
AFEGVVRALLQKPSARVAVLFTRSEDARELLAASQRLNASFTWVASDGWGALESVVAGSE
GAAEGAITIELASYPISDFASYFQSLDPWNNSRNPWFREFWEQRFRCSFRQRDCAAHSLR
AVPFEQESKIMFVVNAVYAMAHALHNMHRALCPNTTRLCDAMRPVNGRRLYKDFVLNVKF
DAPFRPADTHNEVRFDRFGDGIGRYNIFTYLRAGSGRYRYQKVGYWAEGLTLDTSLIPWA
SPSAGPLPASRCSEPCLQNEVKSVQPGEVCCWLCIPCQPYEYRLDEFTCADCGLGYWPNA
SLTGCFELPQEYIRWGDAWAVGPVTIACLGALATLFVLGVFVRHNATPVVKASGRELCYI
LLGGVFLCYCMTFIFIAKPSTAVCTLRRLGLGTAFSVCYSALLTKTNRIARIFGGAREGA
QRPRFISPASQVAICLALISGQLLIVVAWLVVEAPGTGKETAPERREVVTLRCNHRDASM
LGSLAYNVLLIALCTLYAFKTRKCPENFNEAKFIGFTMYTTCIIWLAFLPIFYVTSSDYR
VQTTTMCVSVSLSGSVVLGCLFAPKLHIILFQPQKNVVSHRAPTSRFGSAAARASSSLGQ
GSGSQFVPTVCNGREVVDSTTSSLLEVLFQGPGVQVETISPGDGRTFPKRGQTCVVHYTG
MLEDGKKFDSSRDRNKPFKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHP
GIIPPHATLVFDVELLKLEFAAAHHHHHHHHHH

Sequence of entity 2 (3), FASTA

>8JCY_2 Metabotropic glutamate receptor 3,Serine/threonine-protein kinase mTOR (chains 3)
DYKDDDDKGAPWSHPQFEKGSGSWSHPQFEKLGDHNFLRREIKIEGDLVLGGLFPINEKG
TGTEECGRINEDRGIQRLEAMLFAIDEINKDDYLLPGVKLGVHILDTCSRDTYALEQSLE
FVRASLTKVDEAEYMCPDGSYAIQENIPLLIAGVIGGSYSSVSIQVANLLRLFQIPQISY
ASTSAKLSDKSRYDYFARTVPPDFYQAKAMAEILRFFNWTYVSTVASEGDYGETGIEAFE
QEARLRNICIATAEKVGRSNIRKSYDSVIRELLQKPNARVVVLFMRSDDSRELIAAASRA
NASFTWVASDGWGAQESIIKGSEHVAYGAITLELASQPVRQFDRYFQSLNPYNNHRNPWF
RDFWEQKFQCSLQNKRNHRRVCDKHLAIDSSNYEQESKIMFVVNAVYAMAHALHKMQRTL
CPNTTKLCDAMKILDGKKLYKDYLLKINFTAPFNPNKDADSIVKFDTFGDGMGRYNVFNF
QNVGGKYSYLKVGHWAETLSLDVNSIHWSRNSVPTSQCSDPCAPNEMKNMQPGDVCCWIC
IPCEPYEYLADEFTCMDCGSGQWPTADLTGCYDLPEDYIRWEDAWAIGPVTIACLGFMCT
CMVVTVFIKHNNTPLVKASGRELCYILLFGVGLSYCMTFFFIAKPSPVICALRRLGLGSS
FAICYSALLTKTNCIARIFDGVKNGAQRPKFISPSSQVFICLGLILVQIVMVSVWLILEA
PGTRRYTLAEKRETVILKCNVKDSSMLISLTYDVILVILCTVYAFKTRKCPENFNEAKFI
GFTMYTTCIIWLAFLPIFYVTSSDYRVQTTTMCISVSLSGFVVLGCLFAPKVHIILFQPQ
KNVVTHRLHLNRFSVSGTGTTYSQSSASTYVPTVCNGREVLDSTTSSLLEVLFQGPAILW
HEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTLKETSFNQAYGRDLMEAQE
WCRKYMKSGNVKDLTQAWDLYYHVFRRISKQEF

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	7
Z99	2-[(1S,2S)-2-carboxycyclopropyl]-3-(9H-xanthen-9-yl)-D-alanine	C20 H19 N O5	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Structural insights into dimerization and activation of the mGlu2-mGlu3 and mGlu2-mGlu4 heterodimers. Wang, X., Wang, M., Xu, T. et al. Cell Res (2023) 33:762-774. DOI 10.1038/s41422-023-00830-2 · PubMed

Other PDB entries of the same protein (UniProt P62942 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2PPN 0.92 Å, Crystal structure of FKBP12
2PPP 0.94 Å, Crystal structure of E60Q mutant of FKBP12
6YF3 1.0 Å, FKBP12 in complex with the BMP potentiator compound 10 at 1.00A resolution
6YF2 1.03 Å, FKBP12 in complex with the BMP potentiator compound 6 at 1.03A resolution
8X6P 1.05 Å, Isomerase Protein
6YF1 1.12 Å, FKBP12 in complex with the BMP potentiator compound 8 at 1.12A resolution
8CHM 1.12 Å, Human FKBP12 in complex with (1S,5S,6R)-10-((S)-(3,5-dichlorophenyl)sulfinyl)-3-(pyridin-…
4N19 1.2 Å, Structural basis of conformational transitions in the active site and 80 s loop in the…
8PDF 1.2 Å, FKBP12 in complex with PROTAC 6a2
9LYG 1.26 Å, Crystal structure of FKBP12 complexed with Small Molecule Anchor for Protein-201
2PPO 1.29 Å, Crystal structure of E60A mutant of FKBP12
7U8D 1.39 Å, FKBP12 mutant V55G bound to Rapa*-3Z

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